Analysis of the promoter from an expanding mouse retrotransposon subfamily

Abstract

The mouse genome contains several subfamilies of the retrotransposon L1. One subfamily, T(F), contains 4000-5000 full-length members and is expanding due to retrotransposition of a large number of active elements. Here we studied the T(F) 5' untranslated region (UTR), which contains promoter activity required for subfamily expression. Using reporter assays, we show that promoter activity is derived from T(F)-specific monomer sequences and is proportional to the number of monomers in the 5' UTR. These data suggest that nearly all full-length T(F) elements in the mouse genome are currently competent for expression. We aligned the sequences of 53 monomers to generate a consensus T(F) monomer and determined that most T(F) elements are truncated near a potential binding site for a transcription initiation factor. We also determined that much of the sequence variation among T(F) monomers results from transition mutations at CpG dinucleotides, suggesting that genomic T(F) 5' UTRs are methylated at CpGs.